Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,689,325	T→C	5.7%	T181A (ACA→GCA)	dnaJ ←	Chaperone protein DnaJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,689,325	0	T	C	5.7%	237.5 / 2.7	85	T181A (ACA→GCA)	dnaJ	Chaperone protein DnaJ
Reads supporting (aligned to +/- strand):  ref base T (37/41);  new base C (2/3);  total (41/44)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATA  >  USA300TCH1516_ALE/1689185‑1689465                                                                                                                                             |                                                                                                                                             ttCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTGTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATtgt                                                                                                                                              >  2:793270/1‑141 (MQ=255) ttCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATtgt                                                                                                                                              >  1:894683/1‑141 (MQ=255)  tCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATtgtg                                                                                                                                             <  2:1047202/141‑1 (MQ=255)  tCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATtgtg                                                                                                                                             <  1:860515/141‑1 (MQ=255)   cAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACCTTTCGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTgtgt                                                                                                                                            <  1:982948/141‑1 (MQ=255)      gTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGtttt                                                                                                                                         <  2:716269/141‑1 (MQ=255)      gTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGtttt                                                                                                                                         <  2:404643/141‑1 (MQ=255)         cTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAGGCTTCTTCACATTCTTGACCACTTCCATTACATTTAGGACAAACTAGTTCAGTACGAACTCTACCTAAAATTGTGTTTTgct                                                                                                                                      >  2:904938/1‑139 (MQ=255)         cTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTATGCACTCTACCAAAAATTGTGTTTTGtt                                                                                                                                      >  1:197549/1‑141 (MQ=255)         cTTTCACTGCTAATTTAACTGTTTTATATTCAGTACCTTTTCCGTGACATGTTGGGCAAGCGTCTTCAAATTCTTAACCACTTCCATTACATTTAGGACATACTTGTTCCGTACGAACTCTACCTAAAATTGGGTTTTGtt                                                                                                                                      >  2:944206/1‑141 (MQ=255)          tttCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAAATCTACCTAAAATTGTGTTTTGTTc                                                                                                                                     >  2:1090512/1‑141 (MQ=255)          tttCACTTCTAATTTAACTGTTTCATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTc                                                                                                                                     <  2:321740/141‑1 (MQ=255)          tttCACTTCTAATCTAACTGTTTTCTTGTCAGGGCCTATTCCGTATAAAACATGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTc                                                                                                                                     <  1:520144/141‑1 (MQ=255)            tCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATGTAGGACAAACTTGTTCAGTACGATCTCCACCTAAAATTGTGTTTTGTTCTa                                                                                                                                   <  2:784899/141‑1 (MQ=255)             taCTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTAc                                                                                                                                  <  1:653249/140‑1 (MQ=255)              aCTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACa                                                                                                                                 >  1:438858/1‑141 (MQ=255)              aCTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACa                                                                                                                                 >  2:39140/1‑141 (MQ=255)              aCTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACa                                                                                                                                 >  2:689879/1‑141 (MQ=255)              aCTTCTAATTTAACTCTTTTCTTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAACTTGTGTTTTTTTCTAcc                                                                                                                                 >  1:821483/1‑140 (MQ=255)               cTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTTCTGGGCATTATCGACCAGCCTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCtgtag                                                                                                                                >  1:260105/1‑137 (MQ=255)               cTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAg                                                                                                                                >  1:123368/1‑141 (MQ=255)                   tAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTACAATTGTGTTTTGTTCTACAGCTAc                                                                                                                            >  1:818930/1‑141 (MQ=255)                   tAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTAc                                                                                                                            <  1:906059/141‑1 (MQ=255)                    aaTTTAACTGTTTTATTTTCAGTAGCTTTTCCGTGACACGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACa                                                                                                                           >  1:710710/1‑141 (MQ=255)                    aaTTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACACTACCTAAAATTGTGTTTTGTTCTACAGCTACa                                                                                                                           >  2:330247/1‑141 (MQ=255)                    aaTTCAACTGTCTTATTTTCATGACCTTTTCCGTCACATGTTGCACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACa                                                                                                                           <  1:870001/141‑1 (MQ=255)                      tttAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTCCCTAAAATTGTGTTTTGTTCTACAGCTACATg                                                                                                                         <  2:638913/141‑1 (MQ=255)                          aCTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGCGTTTTGTTCTACAGCTACATGACCa                                                                                                                     >  2:460777/1‑141 (MQ=255)                          aCTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGCGTTTTGTTCTACAGCTACATGACCa                                                                                                                     >  2:460787/1‑141 (MQ=255)                           cTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTTCAGCTACATGACCAg                                                                                                                    >  2:589134/1‑141 (MQ=255)                           cTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTACAAATTCTTGACCACGTCCATTACATTTAGGAAAAACTTGTTAAGTAAGAACTCTACCTAAAATAGAGTTTTGTTCTCCAGCTACATGACCAg                                                                                                                    >  2:722106/1‑141 (MQ=255)                           cTGTTTTATTTTCAGTACCTTTTCCGTGAAATGTTGGACAAGCTTCTTCATATTCTTGACCCCTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACATAAAATTGTGTTTTGTTCTCCAGCTACATGACCAg                                                                                                                    >  2:124321/1‑141 (MQ=255)                            tgcttgaTTTTCATTCCCGTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAATTTGTTCAGTACGATCGCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAgc                                                                                                                   <  2:831166/135‑1 (MQ=255)                            tGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAgc                                                                                                                   <  1:484248/141‑1 (MQ=255)                             gTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAATCTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAgcg                                                                                                                  <  2:739227/141‑1 (MQ=255)                             gTTTTATGTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGCTTTGTTCTACAGCTACATGACCAgcg                                                                                                                  <  2:684694/141‑1 (MQ=255)                                ttATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCa                                                                                                               <  1:384248/141‑1 (MQ=255)                                ttATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAAATGTGTTTTGTTCTACAGCTACATGACCACCGCCa                                                                                                               >  2:959275/1‑141 (MQ=255)                                  aTTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAACCTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACCTGACCGGCGCCAtt                                                                                                             >  2:407261/1‑141 (MQ=255)                                   ttttCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTa                                                                                                            <  1:130685/141‑1 (MQ=255)                                   ttttCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTa                                                                                                            <  2:859373/141‑1 (MQ=255)                                   ttttCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTa                                                                                                            <  1:130688/141‑1 (MQ=255)                                        aatcccTTTTCCGTGACATGTTGGACAAGCTTCTTCAACTTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACGGCTACATGACCAGCGCCATTACAGTa                                                                                                       <  2:221724/137‑1 (MQ=255)                                        aGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGATCAGCGCCATTACAGTa                                                                                                       <  1:550853/141‑1 (MQ=255)                                           aCCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGCCCAGCGCCATTACAGTCACt                                                                                                    >  1:824086/1‑141 (MQ=255)                                           aCCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACt                                                                                                    >  1:238380/1‑141 (MQ=255)                                           aCCTTCTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATAACCAGCGCCATTACAGTAACt                                                                                                    >  2:71903/1‑141 (MQ=255)                                              ttttCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACa                                                                                                 <  1:637534/141‑1 (MQ=255)                                                ttCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAg                                                                                               >  1:515728/1‑141 (MQ=255)                                                 tCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGGCCAGGGTCATTACAGTAACTACAAGt                                                                                              >  1:586211/1‑141 (MQ=255)                                                       actcgTTTGACAAGCTTCTTCAAATTCTTGACCACTTCCCGTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCCTCACAGTAACTACAAGTCttttt                                                                                        <  2:500173/137‑1 (MQ=255)                                                         aTGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTAc                                                                                      >  1:379482/1‑141 (MQ=255)                                                           gTTGGACAAGCTTCTTCAAATTCTTGCCCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACtt                                                                                    <  2:694117/141‑1 (MQ=255)                                                           gTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGCGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACtt                                                                                    <  2:887459/141‑1 (MQ=255)                                                              ggACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGtt                                                                                 <  1:368359/141‑1 (MQ=255)                                                              ggACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGtt                                                                                 <  1:245557/141‑1 (MQ=255)                                                              ggACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGtt                                                                                 <  1:184743/141‑1 (MQ=255)                                                                 cAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCa                                                                              <  1:715994/141‑1 (MQ=255)                                                                    gCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGc                                                                           >  2:544903/1‑141 (MQ=255)                                                                     cttcttCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCt                                                                          >  1:267678/1‑141 (MQ=255)                                                                        cttcAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTg                                                                       <  1:948520/141‑1 (MQ=255)                                                                          tcAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCCGCGCCATTACAGTAACTACAAGACTTTTTACTTGTTCCAGACTTTGca                                                                     >  1:1108652/1‑141 (MQ=255)                                                                          tcAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTCACTACAAGTCTTATTACTTGTTCCAGCCTTTGca                                                                     >  1:506918/1‑141 (MQ=255)                                                                               ttCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGcaccatc                                                                <  2:1101769/141‑1 (MQ=255)                                                                               ttCTTGACCACTTCCATTACATTTAGGACAAACTCGTTCAGTACGAACTCTACCTAAAATTGTGGTTTGTTCTACAGCTTCATGACCAGCGCCATTACAGTTACTATAAGTCTCCATATAGGTTCTATGCTTTGcaccatc                                                                <  2:508344/141‑1 (MQ=255)                                                                                 cTTGACCAATTCCATTACATTTAGGACAAACTTGTTCAGTGCGATCTGTACCTAAAATGGTGTTTTGTTCTACAGCTACATGATCATCGCCATTACAGTCACTACAAGTCTTTTTACTTGTTCCAGGCTTTGcaccatcac                                                              <  2:441794/141‑1 (MQ=255)                                                                                   tGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGcaccatcacca                                                            >  1:446585/1‑141 (MQ=255)                                                                                     aCCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATg                                                          >  1:324036/1‑141 (MQ=255)                                                                                     aCCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATg                                                          >  1:35750/1‑141 (MQ=255)                                                                                       cACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGAc                                                        <  1:449056/141‑1 (MQ=255)                                                                                            cccttACATTTTTGACAATCTTGTTCAGTACGAACTCTGCCTAAAATTGTGTTTTGTTCTACAGCTACATGAGCAGCGCCATTACTGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGtt                                                   <  2:975999/138‑1 (MQ=255)                                                                                            ccATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGtt                                                   >  2:802832/1‑141 (MQ=255)                                                                                                 aCATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCa                                              <  1:925058/141‑1 (MQ=255)                                                                                                       aGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTAc                                        >  2:692459/1‑141 (MQ=255)                                                                                                              aCTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCGTGCTTTGCTGCATCACCATGACATGTCTCGTATGTTCCATCTTTa                                 >  1:783581/1‑141 (MQ=255)                                                                                                              aCTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACCACTTTa                                 >  1:261030/1‑141 (MQ=255)                                                                                                               cTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCTAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTAc                                <  2:710710/141‑1 (MQ=255)                                                                                                               cTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTAc                                <  1:330247/141‑1 (MQ=255)                                                                                                               cTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTAc                                <  1:147808/141‑1 (MQ=255)                                                                                                                ttGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACg                               >  2:954082/1‑141 (MQ=255)                                                                                                                ttGTTCAGTACGAACTCTACCTAAAATTGTGCTGTGTTCTACAGCTACATGACCCGCGCCCTTCCAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGATTCGGCTGTTACATCTTTACg                               >  2:506337/1‑141 (MQ=255)                                                                                                                ttGTTCAGTACGAACTCTACCTAAAATTGCGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACg                               <  1:460787/141‑1 (MQ=255)                                                                                                                ttGTTCAGTACGAACTCTACCTAAAATTGCGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACg                               <  1:460777/141‑1 (MQ=255)                                                                                                                 tGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCTGGCTTTGCACCAGCACCATGACATAGTTCGCATGTTACAACTTTACgg                              >  2:843754/1‑141 (MQ=255)                                                                                                                 tGTTCAGTACGAACACTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGACTTATTACCTGTTCCAGGCTTTGCACCAGCACCATGACATGTTTCGCATGTTACATCTTTACgg                              >  1:270595/1‑141 (MQ=255)                                                                                                                    tCAGTACGAATCCTACCCAAAACTGTCTTTTTTTCCACAGCTACATGACCAGCGTCATTACAGCAACTACAAGTCTTTTTCCTTGTTCCAGGCTTGGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGAtt                           <  2:395614/141‑1 (MQ=255)                                                                                                                         aCGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAAt                      <  1:48626/141‑1 (MQ=255)                                                                                                                                ctACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCtttt               <  1:19249/141‑1 (MQ=255)                                                                                                                                  aCCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTttgt             <  1:39140/141‑1 (MQ=255)                                                                                                                                  aCCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTttgt             <  1:689879/141‑1 (MQ=255)                                                                                                                                            gtgtTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCCGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAAt   >  1:105136/1‑141 (MQ=255)                                                                                                                                            gtgtTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCCTGTTCCCTCTTTCCGGATTGTAATTCCATTtgttgttacgaat   >  2:582249/1‑134 (MQ=255)                                                                                                                                             tgtTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATa  <  1:1090512/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             TTCAGGTACTTTCACTTCTAATTTAACTGTTTTATTTTCAGTACCTTTTCCGTGACATGTTGGACAAGCTTCTTCAAATTCTTGACCACTTCCATTACATTTAGGACAAACTTGTTCAGTACGAACTCTACCTAAAATTGTGTTTTGTTCTACAGCTACATGACCAGCGCCATTACAGTAACTACAAGTCTTTTTACTTGTTCCAGGCTTTGCACCATCACCATGACATGTTTCGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATA  >  USA300TCH1516_ALE/1689185‑1689465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑